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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ), 'gf_id' => 'HOM05D001116', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001116' ), 'data_identifier' => 'HOM05D001116', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001116', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02320' => 'bna', 'A03p06400' => 'bna', 'A06p27970' => 'bna', 'A06p34110' => 'bna', 'A07p03750' => 'bna', 'A10p24370' => 'bna', 'Aa31LG11G14840' => 'aar', 'Aa31LG4G17360' => 'aar', 'Aa31LG5G11150' => 'aar', 'Aa31LG8G14640' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3831' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2071' => 'aag', 'Actinidia07493' => 'ach', 'Actinidia08903' => 'ach', 'Actinidia08904' => 'ach', 'Actinidia09050' => 'ach', 'Actinidia17149' => 'ach', 'Actinidia18316' => 'ach', 'Actinidia19559' => 'ach', 'Actinidia25534' => 'ach', 'Actinidia32007' => 'ach', 'Actinidia36241' => 'ach', 'Actinidia36837' => 'ach', 'Actinidia37729' => 'ach', 'Actinidia40398' => 'ach', 'Ah.02g128940' => 'amhyb', 'Ah.03g136320' => 'amhyb', 'Ah.03g142960' => 'amhyb', 'Ah.07g204600' => 'amhyb', 'AL3G10070' => 'aly', 'AL3G50140' => 'aly', 'AL5G28360' => 'aly', 'AL6G24700' => 'aly', 'Aqoxy39s002' => 'aox', 'Aqoxy3G02105' => 'aox', 'Aqoxy5G00971' => 'aox', 'Aqoxy5G03184' => 'aox', 'Aqoxy7G02371' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3PTW71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86P4B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H7HP3B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KJS60N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NSDN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QT88WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPZJ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VVHX2K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY2X3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR1PS1' => 'arhy', 'AT2G17270' => 'ath', 'AT3G48850' => 'ath', 'AT5G14040' => 'ath', 'ATR0582G252' => 'atr', 'ATR0686G090' => 'atr', 'ATR0807G151' => 'atr', 'Atru.chr3.49' => 'acertr', 'Atru.chr5.3563' => 'acertr', 'Atru.chr6.1898' => 'acertr', 'Atru.chr6.2637' => 'acertr', 'Atru.chr6.2638' => 'acertr', 'Atru.chr6.2673' => 'acertr', 'AUR62003724' => 'cqu', 'AUR62009510' => 'cqu', 'AUR62009511' => 'cqu', 'AUR62010179' => 'cqu', 'AUR62013180' => 'cqu', 'AUR62016575' => 'cqu', 'AUR62034775' => 'cqu', 'AUR62034776' => 'cqu', 'AUR62037839' => 'cqu', 'AUR62041078' => 'cqu', 'BcaB01g05312' => 'bca', 'BcaB01g06349' => 'bca', 'BcaB02g09568' => 'bca', 'BcaB03g16475' => 'bca', 'BcaB08g34720' => 'bca', 'BcaC01g02379' => 'bca', 'BcaC01g02940' => 'bca', 'BcaC06g36250' => 'bca', 'BcaNung06033' => 'bca', 'BolC2t06601H' => 'bol', 'BolC3t13240H' => 'bol', 'BolC3t18082H' => 'bol', 'BolC3t18849H' => 'bol', 'BolC7t41015H' => 'bol', 'BolC9t59144H' => 'bol', 'BraA02t05203Z' => 'bra', 'BraA03t09969Z' => 'bra', 'BraA06t25738Z' => 'bra', 'BraA06t26344Z' => 'bra', 'BraA07t28163Z' => 'bra', 'BraA10t44503Z' => 'bra', 'C02p06540' => 'bna', 'C03p07370' => 'bna', 'C03p58100' => 'bna', 'C03p65910' => 'bna', 'C07p06020' => 'bna', 'C09p63080' => 'bna', 'CAN.G473.154' => 'can', 'CAN.G637.49' => 'can', 'CAN.G647.1' => 'can', 'CAN.G65.100' => 'can', 'CAN.G65.107' => 'can', 'CANSAT25G2574' => 'cansat', 'CANSAT64G0937' => 'cansat', 'CANSAT80G1487' => 'cansat', 'CARHR157660' => 'chi', 'CARHR199320' => 'chi', 'CARHR293660' => 'chi', 'Carub.0003s0007' => 'cru', 'Carub.0003s3122' => 'cru', 'Carub.0005s1502' => 'cru', 'Carub.0006s1223' => 'cru', 'Ca_08126_v3' => 'car', 'Ca_11229_v3' => 'car', 'Ca_17581_v3' => 'car', 'Ca_24995_v3' => 'car', 'Ca_26477_v3' => 'car', 'CBR_g12735' => 'cbr', 'Cc04_g09390' => 'ccan', 'Cc04_g09400' => 'ccan', 'Cc07_g01200' => 'ccan', 'Cc07_g12110' => 'ccan', 'Cc09_g10850' => 'ccan', 'CDE02G1462' => 'cde', 'CDE04G1485' => 'cde', 'CDE05G1943' => 'cde', 'CDE05G3264' => 'cde', 'CDE06G0628' => 'cde', 'CDE08G0407' => 'cde', 'Cfa007108' => 'cfa', 'Cfa007175' => 'cfa', 'Cfa018723' => 'cfa', 'Cfa023899' => 'cfa', 'Ciclev10015678m.g' => 'ccl', 'Ciclev10026550m.g' => 'ccl', 'Ciclev10028883m.g' => 'ccl', 'Ciclev10031869m.g' => 'ccl', 'Ciclev10031895m.g' => 'ccl', 'CiPaw.03G003200' => 'cil', 'CiPaw.04G001800' => 'cil', 'CiPaw.06G115000' => 'cil', 'CiPaw.11G001600' => 'cil', 'ClCG01G007800' => 'cla', 'ClCG02G003350' => 'cla', 'ClCG05G012750' => 'cla', 'ClCG06G018270' => 'cla', 'COL.COLO4_13345' => 'col', 'COL.COLO4_16701' => 'col', 'COL.COLO4_16702' => 'col', 'COL.COLO4_16703' => 'col', 'COL.COLO4_34314' => 'col', 'Cpa.g.c34485' => 'cpa', 'Cpa.g.sc70.82' => 'cpa', 'Cre03.g172300' => 'cre', 'CsaV3_1G000180' => 'csa', 'CsaV3_3G027690' => 'csa', 'CsaV3_5G024870' => 'csa', 'CsaV3_7G001980' => 'csa', 'CSS0001258' => 'camsi', 'CSS0001878' => 'camsi', 'CSS0002356' => 'camsi', 'CSS0002674' => 'camsi', 'CSS0012300' => 'camsi', 'CSS0024217' => 'camsi', 'CSS0032902' => 'camsi', 'CSS0036799' => 'camsi', 'DCAR_002974' => 'dca', 'DCAR_003468' => 'dca', 'DCAR_014478' => 'dca', 'DCAR_025659' => 'dca', 'DCAR_032046' => 'dca', 'Dinv11223' => 'din', 'Dinv14177' => 'din', 'Dinv23204' => 'din', 'Dinv23205' => 'din', 'Dinv23206' => 'din', 'Dinv28301' => 'din', 'Dinv33291' => 'din', 'Duzib084G1445' => 'dzi', 'Duzib132G0207' => 'dzi', 'Duzib147G0089' => 'dzi', 'Duzib187G1526' => 'dzi', 'Duzib205G0035' => 'dzi', 'Duzib248G0581' => 'dzi', 'Duzib264G0930' => 'dzi', 'ECA232G1139' => 'eca', 'ECA233G3566' => 'eca', 'ECA238G0134' => 'eca', 'ECA238G2176' => 'eca', 'ECA246G1686' => 'eca', 'ECA246G3421' => 'eca', 'ECA246G3943' => 'eca', 'ECA247G3786' => 'eca', 'EL10Ac5g11314' => 'bvu', 'EL10Ac5g11315' => 'bvu', 'EL10Ac5g11316' => 'bvu', 'EL10Ac5g11318' => 'bvu', 'EL10Ac6g13384' => 'bvu', 'EL10Ac6g15032' => 'bvu', 'EL10Ac9g21541' => 'bvu', 'Eucgr.E01710' => 'egr', 'Eucgr.G01942' => 'egr', 'Eucgr.H04990' => 'egr', 'Eucgr.I01607' => 'egr', 'Eucgr.I01609' => 'egr', 'Eucgr.J02555' => 'egr', 'Eucgr.L00580' => 'egr', 'FAN02G4567' => 'fan', 'FAN04G2923' => 'fan', 'FAN05G3677' => 'fan', 'FAN08G0991' => 'fan', 'FAN09G2385' => 'fan', 'FAN13G3088' => 'fan', 'FAN14G5639' => 'fan', 'FAN15G0211' => 'fan', 'FAN18G2361' => 'fan', 'FAN24G2084' => 'fan', 'FAN27G1008' => 'fan', 'FvH4_2g16870' => 'fve', 'FvH4_5g09180' => 'fve', 'FvH4_6g54190' => 'fve', 'Glyma.01G157100' => 'gma', 'Glyma.02G065801' => 'gma', 'Glyma.05G201400' => 'gma', 'Glyma.08G008900' => 'gma', 'Glyma.11G087800' => 'gma', 'Glyma.16G050000' => 'gma', 'Glyma.16G050100' => 'gma', 'Glyma.16G146700' => 'gma', 'Glyma.19G101100' => 'gma', 'Gohir.A07G047500' => 'ghi', 'Gohir.A10G071100' => 'ghi', 'Gohir.A10G071150' => 'ghi', 'Gohir.A11G038100' => 'ghi', 'Gohir.A12G013000' => 'ghi', 'Gohir.D07G051700' => 'ghi', 'Gohir.D10G080000' => 'ghi', 'Gohir.D10G080100' => 'ghi', 'Gohir.D11G041400' => 'ghi', 'Gohir.D12G013800' => 'ghi', 'Gorai.001G054800' => 'gra', 'Gorai.007G044500' => 'gra', 'Gorai.008G013800' => 'gra', 'Gorai.011G087100' => 'gra', 'Gorai.011G087200' => 'gra', 'GSVIVG01008630001' => 'vvi', 'GSVIVG01022311001' => 'vvi', 'GSVIVG01023867001' => 'vvi', 'GSVIVG01033005001' => 'vvi', 'HanXRQChr01g0005721' => 'han', 'HanXRQChr02g0034221' => 'han', 'HanXRQChr05g0152961' => 'han', 'HanXRQChr07g0198041' => 'han', 'HanXRQChr07g0198051' => 'han', 'HanXRQChr09g0273971' => 'han', 'HanXRQChr10g0316211' => 'han', 'HanXRQChr12g0356581' => 'han', 'HanXRQChr12g0356591' => 'han', 'HanXRQChr14g0451321' => 'han', 'HanXRQChr14g0451331' => 'han', 'HanXRQChr15g0475751' => 'han', 'HanXRQChr15g0479831' => 'han', 'HanXRQChr17g0550801' => 'han', 'Haze_03638' => 'cav', 'Haze_07115' => 'cav', 'Haze_14936' => 'cav', 'Haze_27358' => 'cav', 'Hma1.2p1_0032F.1_g018750' => 'hma', 'Hma1.2p1_0168F.1_g074090' => 'hma', 'Hma1.2p1_0168F.1_g074100' => 'hma', 'Hma1.2p1_0421F.1_g150000' => 'hma', 'Hma1.2p1_1387F.1_g279910' => 'hma', 'HPP92_005943' => 'vpl', 'HPP92_007018' => 'vpl', 'HPP92_009510' => 'vpl', 'HPP92_022182' => 'vpl', 'HPP92_022196' => 'vpl', 'Hund04211' => 'sun', 'Hund06360' => 'sun', 'Hund10064' => 'sun', 'Lalb_Chr02g0156811' => 'lal', 'Lalb_Chr04g0246911' => 'lal', 'Lalb_Chr05g0214941' => 'lal', 'Lalb_Chr12g0202391' => 'lal', 'Lalb_Chr13g0297031' => 'lal', 'Lalb_Chr14g0364011' => 'lal', 'Lalb_Chr16g0380171' => 'lal', 'Lalb_Chr22g0359991' => 'lal', 'Lj1g0008285' => 'lja', 'Lj2C504G4' => 'lonja', 'Lj2g0009111' => 'lja', 'Lj2g0014449' => 'lja', 'Lj4g0002774' => 'lja', 'Lj5A89T39' => 'lonja', 'Lj5C171G24' => 'lonja', 'Lj7C616T12' => 'lonja', 'Lj9A484G64' => 'lonja', 'LjContig00081g0004922' => 'lja', 'Lsat_1_v5_gn_0_12221' => 'lsa', 'Lsat_1_v5_gn_0_46081' => 'lsa', 'Lsat_1_v5_gn_1_32300' => 'lsa', 'Lsat_1_v5_gn_2_94540' => 'lsa', 'Lsat_1_v5_gn_3_48521' => 'lsa', 'Lsat_1_v5_gn_4_84001' => 'lsa', 'Lsat_1_v5_gn_5_10300' => 'lsa', 'Manes.02G115800' => 'mes', 'Manes.04G092000' => 'mes', 'Manes.06G125300' => 'mes', 'Manes.11G078100' => 'mes', 'Manes.14G046100' => 'mes', 'Manes.15G114500' => 'mes', 'Mapoly0012s0114' => 'mpo', 'Mapoly0085s0103' => 'mpo', 'Mapoly0121s0027' => 'mpo', 'Mapoly0136s0026' => 'mpo', 'MBI06_g23365_MAGBIO' => 'mbi', 'MBI07_g40346_MAGBIO' => 'mbi', 'MBI11_g08162_MAGBIO' => 'mbi', 'MBI11_g43868_MAGBIO' => 'mbi', 'MBI11_g43982_MAGBIO' => 'mbi', 'MCO09G134' => 'mco', 'MCO11G462' => 'mco', 'MD05G1139900' => 'mdo', 'MD06G1133000' => 'mdo', 'MD09G1004400' => 'mdo', 'MD10G1074500' => 'mdo', 'MD10G1142200' => 'mdo', 'MD14G1149100' => 'mdo', 'MD14G1149200' => 'mdo', 'MD17G1007900' => 'mdo', 'Medtr4g094578' => 'mtr', 'Medtr5g024770' => 'mtr', 'Medtr6g033280' => 'mtr', 'Medtr7g083790' => 'mtr', 'Medtr8g099910' => 'mtr', 'MELO3C014803.2' => 'cme', 'MELO3C026171.2' => 'cme', 'MELO3C028882.2' => 'cme', 'MELO3C033942.2' => 'cme', 'Migut.D01223' => 'egut', 'Migut.F00018' => 'egut', 'Migut.K01482' => 'egut', 'Migut.N01361' => 'egut', 'Migut.O00348' => 'egut', 'MSTRG.22878' => 'ama', 'MSTRG.27613' => 'ama', 'MSTRG.3046' => 'ama', 'MSTRG.9349' => 'ama', 'Nitab4.5_0000495g0030' => 'nta', 'Nitab4.5_0000519g0280' => 'nta', 'Nitab4.5_0000783g0040' => 'nta', 'Nitab4.5_0002172g0140' => 'nta', 'Nitab4.5_0004269g0030' => 'nta', 'Nitab4.5_0004728g0070' => 'nta', 'Nitab4.5_0005533g0040' => 'nta', 'Nitab4.5_0007491g0020' => 'nta', 'Nitab4.5_0015580g0010' => 'nta', 'Nn3g16309' => 'nnu', 'Nn4g22177' => 'nnu', 'Nn5g31031' => 'nnu', 'Oeu003427.1' => 'oeu', 'Oeu013473.1' => 'oeu', 'Oeu019025.1' => 'oeu', 'Oeu039793.1' => 'oeu', 'Oeu058118.1' => 'oeu', 'Os02g0767500' => 'osa', 'Os03g0263400' => 'osa', 'Os04g0448800' => 'osa', 'Os06g0210500' => 'osa', 'Os09g0454600' => 'osa', 'Os09g0554000' => 'osa', 'Peaxi162Scf00171g01025' => 'pax', 'Peaxi162Scf00362g10019' => 'pax', 'Peaxi162Scf00420g00847' => 'pax', 'Peaxi162Scf01064g00023' => 'pax', 'Peaxi162Scf01064g00024' => 'pax', 'Peaxi162Scf01393g00017' => 'pax', 'PGR042G3264' => 'pgr', 'PGR083G0212' => 'pgr', 'PGR119G0295' => 'pgr', 'PGR142G2003' => 'pgr', 'PGSC0003DMG400018680' => 'stu', 'PGSC0003DMG400020196' => 'stu', 'PGSC0003DMG400027043' => 'stu', 'PGSC0003DMG400034083' => 'stu', 'PGSC0003DMG401014665' => 'stu', 'Phvul.001G086600' => 'pvu', 'Phvul.002G118300' => 'pvu', 'Phvul.002G282900' => 'pvu', 'Phvul.004G070500' => 'pvu', 'Potri.001G322300' => 'ptr', 'Potri.004G207200' => 'ptr', 'Potri.005G098800' => 'ptr', 'Potri.009G168550' => 'ptr', 'Potri.012G105100' => 'ptr', 'Potri.015G104400' => 'ptr', 'Potri.017G060800' => 'ptr', 'Pp3c11_9290' => 'ppa', 'Pp3c11_9520' => 'ppa', 'Pp3c13_9800' => 'ppa', 'Pp3c25_2448' => 'ppa', 'Pp3c25_2450' => 'ppa', 'Pp3c26_9770' => 'ppa', 'Pp3c3_7930' => 'ppa', 'Pp3c7_18320' => 'ppa', 'Pp3c7_18360' => 'ppa', 'Pp3c8_21830' => 'ppa', 'PRCOL_00004861' => 'pco', 'PRCOL_00005713' => 'pco', 'Prupe.3G312300' => 'ppe', 'Prupe.5G143800' => 'ppe', 'Prupe.5G144200' => 'ppe', 'Prupe.8G180700' => 'ppe', 'Psat1g097600' => 'psa', 'Psat2g000640' => 'psa', 'Psat2g147680' => 'psa', 'Psat3g094120' => 'psa', 'Psat7g038880' => 'psa', 'PSO017G5046' => 'pso', 'PSO170G4420' => 'pso', 'PSO210G5186' => 'pso', 'PSO384G0946' => 'pso', 'PSO443G0004' => 'pso', 'PSO443G0042' => 'pso', 'PSO478G5269' => 'pso', 'QL02p069916' => 'qlo', 'QL02p069930' => 'qlo', 'QL02p100381' => 'qlo', 'QL06p053317' => 'qlo', 'QL10p001000' => 'qlo', 'QL11p056489' => 'qlo', 'RcHm_v2.0_Chr2g0176371' => 'rch', 'RcHm_v2.0_Chr3g0469101' => 'rch', 'RcHm_v2.0_Chr6g0281001' => 'rch', 'RcHm_v2.0_Chr7g0189001' => 'rch', 'Rhsim05G0046500' => 'rsi', 'Rhsim08G0039900' => 'rsi', 'Rhsim08G0195500' => 'rsi', 'Rhsim10G0001900' => 'rsi', 'Rhsim10G0191700' => 'rsi', 'RhsimUnG0141000' => 'rsi', 'RhsimUnG0170700' => 'rsi', 'Sabra04G0139500' => 'sbr', 'Sabra05G0081200' => 'sbr', 'Sabra12G0077500' => 'sbr', 'Sabra15G0124100' => 'sbr', 'Sabra16G0204500' => 'sbr', 'Sabra17G0054200' => 'sbr', 'SalBow1G4586' => 'sbo', 'SalBow4G1454' => 'sbo', 'SalBow5G0145' => 'sbo', 'SalBow5G0349' => 'sbo', 'SalBow5G3067' => 'sbo', 'SalBow5G3098' => 'sbo', 'Sc03g0004850' => 'sci', 'Sc04g0000280' => 'sci', 'Sc08g0002130' => 'sci', 'Sed0001999' => 'sed', 'Sed0008009' => 'sed', 'Sed0024154' => 'sed', 'Sed0025935' => 'sed', 'Sed0027617' => 'sed', 'SEGI_05217' => 'sgi', 'SEGI_06411' => 'sgi', 'SEGI_08932' => 'sgi', 'SEGI_11067' => 'sgi', 'SEGI_16742' => 'sgi', 'SEGI_22923' => 'sgi', 'SEGI_22996' => 'sgi', 'SEGI_29796' => 'sgi', 'SEGI_29927' => 'sgi', 'SEGI_32437' => 'sgi', 'SEGI_35931' => 'sgi', 'SGA_v2.0_scaffold34G13693' => 'sas', 'SGA_v2.0_scaffold40G15602' => 'sas', 'SGA_v2.0_scaffold47G17629' => 'sas', 'SGA_v2.0_scaffold74G24694' => 'sas', 'SGA_v2.0_scaffold98G29304' => 'sas', 'SMO228G0008' => 'smo', 'SMO230G0061' => 'smo', 'SMO356G0284' => 'smo', 'SMO356G0353' => 'smo', 'Solyc02g094470.3' => 'sly', 'Solyc03g097840.3' => 'sly', 'Solyc06g072510.4' => 'sly', 'Sopen02g039130' => 'spe', 'Sopen03g005880' => 'spe', 'Sopen03g028580' => 'spe', 'Sopen06g028880' => 'spe', 'Sp3g00090' => 'spa', 'Sp3g30620' => 'spa', 'Sp5g13200' => 'spa', 'Sp6g29960' => 'spa', 'TAR371G0232' => 'tar', 'TAR622G0139' => 'tar', 'TAR625G0120' => 'tar', 'TAR629G0121' => 'tar', 'TAR629G2879' => 'tar', 'THA.LOC104802369' => 'tha', 'THA.LOC104804298' => 'tha', 'THA.LOC104807407' => 'tha', 'THA.LOC104819726' => 'tha', 'THA.LOC104821534' => 'tha', 'THA.LOC104822419' => 'tha', 'Thecc.01G002500' => 'tca', 'Thecc.02G146600' => 'tca', 'Thecc.03G138200' => 'tca', 'Thecc.04G045400' => 'tca', 'Thhalv10010467m.g' => 'esa', 'Thhalv10013819m.g' => 'esa', 'Thhalv10020809m.g' => 'esa', 'Thhalv10022786m.g' => 'esa', 'TPR.G12824' => 'tpr', 'TPR.G17459' => 'tpr', 'TPR.G18646' => 'tpr', 'TPR.G33777' => 'tpr', 'TPR.G36690' => 'tpr', 'TPR.G8975' => 'tpr', 'TWI09G0347' => 'twi', 'TWI14G0318' => 'twi', 'TWI23G1152' => 'twi', 'TWI31G0457' => 'twi', 'TWI32G0976' => 'twi', 'TWI39G0498' => 'twi', 'unitig_0.g2576' => 'ugi', 'unitig_746.g26875' => 'ugi', 'unitig_88.g27696' => 'ugi', 'unitig_88.g27786' => 'ugi', 'vmacro10799' => 'vma', 'vmacro17309' => 'vma', 'vmacro18371' => 'vma', 'vmacro19162' => 'vma', 'vmacro19163' => 'vma', 'vmacro20610' => 'vma', 'vmacro22238' => 'vma', 'VMungo0251G1357' => 'vmu', 'VMungo0464G2122' => 'vmu', 'VMungo1215G0584' => 'vmu', 'VMungo1383G1734' => 'vmu', 'Zm00001eb011580' => 'zma', 'Zm00001eb012490' => 'zma', 'Zm00001eb039070' => 'zma', 'Zm00001eb104460' => 'zma', 'Zm00001eb150310' => 'zma', 'Zm00001eb193580' => 'zma', 'Zm00001eb231600' => 'zma', 'Zm00001eb256020' => 'zma', 'Zm00001eb314770' => 'zma', 'Zm00001eb331840' => 'zma', 'Zm00001eb408410' => 'zma' ) $gf_id = 'HOM05D001116' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001116' ) $data_identifier = 'HOM05D001116' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 13, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 10, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 8, 'bvu' => (int) 7, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 10, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 11, 'sas' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408410' $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